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Jadzia Dax is in Quark's showing off magic tricks to Quark and Julian Bashir when CaptainBenjamin Sisko calls her away. He informs her that a Trill science team is coming to create an artificial wormhole and that the leader of the team is Lenara Kahn. He then suggests that Dax has three months of leave accumulated and that she should take advantage of it. But Dax says she can handle it and that she has never allowed her past lives to interfere with her job.

Dax, Worf, and Kira Nerys greets the science team comprised of Dr. Hanor Pren, Dr. Lenara Kahn, and her brother Dr. Bejal Otner. Dax and Kahn formally greet and both agree "it's been a long time". Dax reveals to a curious Major Kira that Kahn used to be Dax's wife.

In Quark's, Kira and Bashir explain to a confused Quark that Dax's previous host Torias was married to Kahn's previous host Nilani. However Torias was killed in a shuttle accident and Nilani became a widow. When Nilani died, the Kahn symbiont passed on to Lenara. Kira can not understand why Dax and Kahn can not simply "pick up where they left off", but Bashir explains that it is strictly against the rules of Trill society to acknowledge it in any way. Rekindling a relationship with a love from a past life is called Reassociation, and the Trill feel it is unnatural as the point of joining is to allow the symbiont to accumulate experiences from many lifetimes. When moving from host to host, the symbiont must learn to let go of the past and move on from family and loved ones. Kira believes there must have been some Trill who have reassociated and there have: they were exiled from Trill society and their symbionts died with them. There is nothing more important for a joined Trill than to protect the life of the symbiont and therefore Bashir believes Dax will not act on any feelings she has.

At the welcome reception for the Trill scientists, Dax and Kahn have an awkward encounter at the buffet table which is not helped by the inquisitive looks cast by everyone else in the room. Dax humorously suggests getting in a screaming match to entertain the audience. Kahn jokes that perhaps they could throw themselves at each other, profess their love and disregard for Trill society. Kahn adds that they are both mature adults who are capable of handling the situation and Dax agrees.

On the USS Defiant, the science team is going over the plan to generate a subspace tensor matrix with a magneton pulse to create an opening in the space-time continuum. Left alone on the bridge, Kahn and Dax discover a few problems, and Dax tells Kahn not to panic – Torias used to tell Nilani that she was making a fuss over nothing and panicking. Dax admits that Torias was insensitive but Nilani overreacted as well. Kahn replies defensively and accidentally in the first person, but what she meant to say was "Torias being a pilot made Nilani nervous". Both hosts feel they have never had so much trouble separating their feelings from that of a past host. Dax adds that Torias was at fault for testing an unsafe shuttle and that the part of her that is Torias is very sorry. On impulse, Dax invites Kahn to dinner with her and Bashir, only it turns out that Dax nominated Bashir as a chaperon without asking first. Kahn agrees to meet that night at Quark's.

"I think he had a good time"

It turns out Bashir had plans that night, but Dax insists he cancel them and he relents. The unfortunate Bashir sits at a table yawning, completely left out while Kahn and Dax reminisce the night away. Bashir gets called away by EnsignTyler's broken leg and leaves a little too eagerly. Kahn thinks that Bashir is a good friend, listening to them trading stories and not complaining. Kahn gives Dax her pair of Klingon earrings and Dax reaches out to hold Kahn's hand, only to be observed by Dr. Pren.

"Defiant Log, stardate 49195.5. Lieutenant Commander Worf reporting. We have arrived at the coordinates to begin preliminary tests for the artificial wormhole project. A Trill science delegation has offered to help, and we've granted them access to the Defiant".

On the Defiant, preliminary testing has begun. Pren reports to Dr. Otner about the former couples' dinner date the previous night and observes they are very friendly towards each other. Dax embraces Kahn as the first test succeeds: the wormhole was open for 23.4 seconds.

While Otner and Kahn have dinner, Otner asks questions about Dax, who visited Kahn's quarters the previous night. Kahn becomes defensive and Otner states that people are starting to notice how Kahn and Dax are acting towards each other. Kahn storms off angrily and Otner apologizes. He agrees to trust her if she says that nothing is going on, and Lenara insists there is not.

Kahn visits Dax's quarters considerably upset at the encounter with her brother. Dax suggests they should not see each other and they should not be having this conversation but Kahn says that would not change their feelings. Kahn admits that she has not gotten over Dax and Dax tells Kahn she has missed her so much. They share a passionate kiss and Kahn quickly leaves afterward.

Dax seeks Benjamin Sisko's advice regarding what to do. Sisko thinks Dax should not pursue the relationship as Curzon Dax had said that the price for violating the reassociation taboo is too high. Sisko wants Dax to think about what will happen if they reassocciate: when Jadzia dies. Sisko assures her that if he were in her position he would want to be certain that he can pay the price before doing anything. Sisko, however, agrees to back Dax if she is sure that this is what she wants. Dax says that in her seven lifetimes, she has never had a friend quite like Sisko.

On the Defiant, the team launches another attempt to send an object through the artificial wormhole. The wormhole appears to be stable and a probe is launched. It causes a large explosion on the Defiant with a hull breach on Deck 5 and plasma leaks in the engine room where Dr. Kahn is located. The bridge cannot contact the engine room and Dax goes to investigate. The leak is out of control and the plasma needs to be vented out to space, however Kahn is lying out of reach and unconscious. Dax walks on a level 8 force field over the leaked plasma and gets to Kahn in just in time with the help of Michael Eddington. The plasma is vented before it damages the warp core. Kahn tells Dax that she does not want to lose her again and Dax agrees.

Dax visits the recovering Kahn and Otner thanks Dax for what she did. He leaves and gives them their privacy. Dax gives Kahn a bottle of Risianperfume and says that the accident may have been caused by the tetryon field's reaction to the probe's shielding, producing a massive graviton wave. Kahn feels guilty about the damage but Dax says it is a huge achievement. Dax then suggests Kahn do further research with her at Deep Space 9 instead of returning to Trill and that she is prepared to pay the price. Dax says it does not matter what everyone else thinks, but what they feel is most important. Kahn however feels that she can not give up everything she worked for and ignore the rules, despite feeling that a part of her is missing without Dax. Kahn wants to think it over on Trill for a little longer, but Dax says that if Kahn leaves on the transport tomorrow they both know that she will probably never return.

Worf escorts Pren and Otner to the airlock while Dax observes from above, still hoping Kahn will stay. However Kahn arrives soon after. She casts one last lingering look at Dax and the grief-stricken hosts part, possibly forever.

"What do Klingons dream about?"
"Things that would send cold chills down your spine, and wake you in the middle of the night. No, it is better that you do not know. Excuse me."
"I can never tell when he's joking."

- Kira and Worf

"I'm not like you, Dax... I don't have a little Curzon inside me telling me to be impulsive... to ignore the rules... give up everything I've worked for..."
"Can you really walk away from me... from us? After all this time we're back together. Don't throw that away."
"I don't want to... Maybe I need more time... maybe if I go back to Trill for a while... think it over... I could always come back later..."
"I wish I could believe you. But ultimately, it comes down to this... if you feel about me the way I feel about you... you won't get on that transport tomorrow. And if you do leave... I think we both know you're never coming back."

The idea for the taboo regarding former Trill lives was Michael Piller's. He developed the concept early in the second season, but it never made it on-screen. René Echevarria explains Piller's idea by saying, "He felt they'd have a very strict taboo in order to avoid an aristocracy of the joined. Otherwise, they'd only want to hang out with each other, their dear old friends from five hundred years ago, and it would become a really screwed up society." (Star Trek: Deep Space Nine Companion)

In the original version of the story, Kahn was a man. It was Ronald D. Moore who suggested making Kahn a woman.

Avery Brooks directs a scene with Terry Farrell and Susanna Thompson on the Defiant bridge set.

This episode features Star Trek's first same-sex kiss and is one of the most controversial episodes in the show's history. According to Ronald D. Moore, "some felt betrayed, didn't want to see this in their homes. An affiliate down south cut the kiss from their broadcast." Similarly, René Echevarria says, "my mother was absolutely scandalized by the episode. Shocked and dismayed. She told me 'I can't believe you did that. There should have been a parental guidance warning'." Steve Oster says that a man called the show and complained, "you're ruining my kids by making them watch two women kiss like that." Much of the public response mirrored that of the famous Kirk-Uhura kiss in the original series episode TOS: "Plato's Stepchildren". (Star Trek: Deep Space Nine Companion)

There is a story regarding the man complaining about his kids seeing the kiss: It was a production assistant who took the call. After hearing the man's complaint, the PA asked if the man would've been okay with his kids seeing one woman shoot the other. When the man said he would be okay with that, the PA said "You should reconsider who's messing up your kids". (Star Trek: Deep Space Nine Companion)

Both cast and crew stand by the idea that this episode was not actually about homosexuality, any more than "Plato's Stepchildren" was about inter-racial relationships. Director Avery Brooks is very clear about this: "it was a story about love, and the consequences of making choices out of love. The kiss was irrelevant." Just as clear is writer René Echevarria "we could tell the story without ever talking about the fact that they are two women." Ronald D. Moore makes a similar point: "it deals with homosexuality and sexual orientation and tolerance, but I'm very proud of the fact that nowhere in the episode does anyone even blink at the fact that these are two women. That's the part that sails by everyone on the show." Finally, Ira Steven Behr points out, "We're not doing a show about lesbians, we're doing a show about Trills." (Star Trek: Deep Space Nine Companion)

Avery Brooks reinforces the notion that this is just a simple love story in Charting New Territory: Deep Space Nine Season Four, a documentary in the special features of the DS9 Season 4 DVD; "It's a love story after all. What's extraordinary about it, you know, the love of your life, and somehow that love is taken away, and you have a chance, another chance, you know, a hundred and fifty years later, to be together again. It was an extraordinary story. I thought it was important that we tell this story honestly and truthfully about love, and so it's not about sex, or same gender or any of the above, even though, obviously, in our world, that's what people started to look at, but I mean it was so important for me to tell that story honestly and truthfully, especially for the people who have suffered, you know, in our world, needlessly, because of love. I was adamant that we were not going to sensationalize this kiss, because, again, I mean, you know, for Star Trek I suppose, or even at that time, you know, for television, prime time television, it was a big deal."

Also in the Charting New Territory documentary, Terry Farrell reiterates the fact that 'lesbianism' is not an issue in the episode; "I think because "Rejoined" was such a sensitive subject, it was very important to show that it was just a choice, and no one judged Dax for her choice, and everyone supported her as a friend, and they were really concerned about her heart getting broken, because she was going to have to give up being a joined Trill. She was going to be banished from her land, she'd have to change her way of life, but not because of her love for this woman, but because it was from the past. It was appropriate for my character to have this moment, it wasn't the 'big lesbian kiss' to get you to watch Star Trek: Deep Space Nine, and of course my character could run up against something like this and it would make sense. And it's an interesting, topical, very Gene Roddenberry-esque way to have the show done."

In the same documentary, Ronald D. Moore makes a similar point; "To the audience, you're playing out this metaphor of a taboo that you're not supposed to be involved with somebody, and the audience sees these two women who are in love together, but the show will never ever comment on it, because it's really about this Trill taboo, this completely other issue. But the idea of homosexual love is staring the audience in the face no matter what they do, but we never have to mention it in the show. It just became this lovely tale about these two forbidden lovers that just couldn't get over that one had died and didn't get a chance to say goodbye, and here they come together in these two other bodies, but what they once felt for one another is still there, but the societal taboo was so strong that one of them had to back out, one of them wasn't willing to take it all the way. It was just a lovely bit of Star Trek because it really was an allegory for our society, and that's ultimately what Trek does best."

"Rejoined" is one of Terry Farrell's favorite episodes due to the message behind it. Farrell commented that it was: "a lost love episode, absolutely. I'm so glad we got to do it. It was an important show. It's interesting to see how people react to 'Rejoined'. I like the idea of sending people a bigger message than they're used to seeing on TV, something that makes them think and gives them something to talk about. I think the show is so appropriate for Dax, more appropriate than for anything other character on television. That's because Dax has always had this duality. She has been a man and a woman several times. Any entity that has that duality is going to have some controversy surrounding it, even though the the story is not about a gay relationship. I have several friends that are gay and I don't judge them for that. In fact, I applaud their honesty. I applaud anyone who is honest about how they feel and who they are. It's not easy for most gay people to be honest about it because they're often treated poorly. I feel badly for people who stay in the closet and secretly feel like they're living another life and can't tell their friends of family". (The Official Star Trek: Deep Space Nine Magazine Vol. 14)

Farrell also liked the way all of the resistance and controversy which Dax and Lenara Kahn face from others is inspired by taboos in Trill culture, and has nothing to do with gender or lesbianism. She also admired the way that director Avery Brooks directed the kiss in a non-sensationalist manner. (Crew Dossier: Jadzia Dax, DS9 Season 2 DVD, Special Features) Of his direction of the kiss, Brooks has said, "People want to hype stuff like that, but I wasn't going to have it." (Star Trek: Deep Space Nine Companion)

Susanna Thompson was also a fan of Avery Brooks' directions of this episode; "It was my first time working on Star Trek where a director wanted me to come in prior to the first day you start shooting, and so he got Terry and I together. I felt very safe with him. And being an actor, he understood all the technical ramifications that you're sort of distracted with on any given day. But he also knew that this episode was going to be a little controversial because there was a same sex kiss. He was so good at keeping us safe and protected, but also giving us such a great space to be brave." (Hidden File 04, DS9 Season 4 DVD, Special Features)

On one especially odd complaint that was received, Ira Steven Behr commented "the favorite of mine, and I haven't seem them all - was that we were taken to task for seeming to support lesbianism and reincarnation on the show... this was from some minister somewhere. So, yeah - this 'reincarnation' thing with the Trills... its dangerous! It's seeping into the minds of America's youth! ("The Behr Necessities", Star Trek Monthly, issue 12)

The themes of a Trill continuing a relationship after changing hosts explored here are similar to those in TNG: "The Host", the Trills' introductory episode. The situation here differs in that both parties are joined Trills, changing the dynamic dramatically.

Contrary to Jadzia's proclamation, she had actually twice previously let her past lives get in the way of her work, once in DS9: "Dax" and again in DS9: "Blood Oath", although this was the first time confronting the taboo against romance.